This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our overall goal is to define the microbial populations found in the cystic fibrosis (CF) lung using "deep sequencing" methodologies. The chronic bacterial infections associated with the CF lung contribute to the long-term damage to the lungs of these patients, resulting in respiratory failure. While Pseudomonas aeruginosa and Staphylococcus aureus are the primary pathogens in the CF lung, there is evidence emerging that additional pathogens can contribute to disease outcome, and furthermore, microbial populations may shift upon exacerbation of infection and subsequent treatment of the exacerbations. These exacerbations lead to progress loss of lung function, and eventually to the death of CF patients due to respiratory failure. Detailed studies of shifts in microbial populations over the course of stable infection, exacerbations and post-treatment regimens have not been assessed. Thus, our central hypothesis is that important bacterial pathogens responsible for causing reduction of lung function in CF patients have not yet been identified. A better understanding of the microbial populations under these varied conditions may help facilitate treatment of these chronic infections in the CF lung. In this study, we aim to analyze the bacterial populations within expectorated sputum from patients with stable infections, as well as patients undergoing exacerbations before and after antibiotic therapy. This study represents a collaboration between Drs. George O'Toole, Bruce Stanton, Deborah Hogan (Dartmouth Medical School) and Dr. Worth Parker and colleagues (DHMC). The 454 sequencing will be performed by Dr. Mitch Sogin at WHOI using bacterial DNA prepared at Dartmouth.